Exploring suitable maize straw-return measures is essential for the new double-cropping system of maize (Zea mays L.)–rice (Oryza sativa L.) rotation in the middle reaches of Yangtze River in China, which can increase crop yield by improving soil quality. In this study, four straw-return measures were evaluated by investigating the soil bulk density (BD), organic matter (OM), microbial community, and nutrients from 2016 to 2018. The four straw-return treatments were as follows: (1) no straw-return (CK), (2) only rice straw incorporated into the field (M0Ri), (3) both maize and rice straw incorporated to field (MiRi), and (4) maize straw mulched and rice straw incorporated into the field (MmRi). Compared to CK, two-season crop straw-return treatments changed soil microbial community composition, and increased soil total organic carbon (TOC) and dissolved organic carbon (DOC), microbial biomass carbon (MBC), mineralized nitrogen (Nmin), available phosphorus (P) and exchangeable potassium (K) in the 0–20 cm soil layer by 3.6%, 63.4%, 38.8%, 12.4%, 39.7%, and 21.6%, respectively, averaged across MmRi and MiRi treatments. In addition, MmRi and MiRi increased annual yield by 9.1% and 15.2% in 2017 and 11.7% and 12.9% compared to CK in 2018, respectively. MmRi exhibited superiority in the soil microbial community, enzyme activities, DOC, MBC, Nmin, available P, and exchangeable K in contrast to MiRi. We concluded that MmRi is the best measure to implement for straw-return in maize–rice rotation systems.